A genetic mutation that leads to a nucleotide repeat expansion (NRE) of repetitive DNA on chromosome 9 in protein reading frame 72 (C9orf72) has been associated with a number of age-related neurodegenerative diseases: Lou Gehrig's disease (ALS), frontal temporal dementia (FTD), Alzheimer's disease, and a phenocopy of Huntington's disease. Recent advances in our molecular understanding of the C9orf72 NRE mutation has demonstrated this NRE also shares many cellular defects found in other NRE-linked neurological diseases, such as Fragile X, many ataxias, and Huntington's disease. Therefore, the research proposed here will examine the molecular defects caused by NREs using the C9orf72 NRE paradigm. The research will investigate three important aspects to advance the understanding of NRE-linked defects. First, proteins that bind to the non-canonical structures formed by the DNA and RNA of the C9orf72-NRE will be examined for their mechanism(s) of recognition, and the cellular defects that result from the nucleotide*protein complex will be determined in patients cells and tissues. Second, the non-canonical nucleotide structures formed by the C9orf72 NRE can endanger genome stability. Therefore, the relationship between nucleotide structures and DNA damage for the C9orf72 NRE will be addressed using in vitro biochemical experiments, and examined in patient cells and tissues. The final work proposed here will identify ligands that bind to non-canonical nucleotide structures formed by the C9orf72 NRE to prevent the downstream NRE-linked cellular defects. This will be performed using a thorough biophysical characterization of nucleotide*ligand complexes and nucleotide*protein complexes in the presence of ligands. Promising ligand candidates will then be examined for their efficacy in patient induce-pluripotent stem motor neuron cells and in Drosophila expressing a transgenic C9orf72 NRE. In summary, the proposed work will advance our molecular understanding of the chronic molecular stresses caused by the C9orf72 NRE that lead to the age-related neurodegenerative defects, and it will identify potential disease modifying ligands.